Sped up py transform and rdf generation by not precomputing visible nodes and calling eval on nonprecompiled code

Created Neighbor interface to enable discovering nodes by hnodeids from
a given node
Precompiled the transform code call and used set on the interpreter
instead of exec to add variables to the python workspace
Optimizred collectNodes
Speed ups
Reset workspace between batches of offline rdf generation

Refactored out some commonality between the rdf generators.

Cleaned up some exception handling (not every import needs to be able
to throw a SQLException)
Replaced regex in normalizeURI with a hand coded replacement method

Also, we don't rebuild the URI unless we find a problem.
Merge branch 'development' of github.com:InformationIntegrationGroup/Web-Karma into pytransform_speedup

need pytransform command checking for adding new columns
Add some error checking to AddColumnCommand
Fixed a reinitialization bug for offline database rdf generation
ArrayList fixes for speedup
Optimized Semantic Type Suggestion

Now disabled in offline rdf generation

Only compute suggestions on single column when we add columns instead
of whole table.

Optimized sampling of examples for semantic types.

Fixed issue with unsetting semantic type when no semantic type is set.
Replaced toCharArray to charAt

toCharArray makes a copy.
Tentative fix for out of order json
Prevent duplicate Transformation tags from being appended to py transform command

o SubmitPyTransformationCommand and processed by
Worksheet2RMLJenaModelParser
Lots of refactoring

maybe all for naught.
Removed commented out code
Merge branch 'pytransform_speedup' into worksheet_history_cleanup
Merge branch 'development' into worksheet_history_cleanup
Remove checkHistory, hideModel, transformations from DataSourcePublisher, and uuid generator

Removed checkHistory from ShowModel, ShowAutoModel, and SplitColumn on
server and client side
Removed hideModel
Added call to showDialogForLoadModel so that importdb now shows model
Removed transformations from DataSourcePublisher
Revert back to incremental id generation
Merge branch 'worksheet_history_cleanup' into pytransform_speedup
Merge branch 'pytransform_speedup' into development

Fixed publishing r2rml model because the directory does not exist
anymore because of the gitignore additions.  a previous fix fixed
publishing rdf.